Reducing intron retention

Abstract

Disclosed herein are methods, compositions, polynucleic acid polymers, assays, and kits for inducing processing of a partially processed mRNA transcript to remove a retained intron to produce a fully processed mRNA transcript that encodes a full-length functional form of a protein. Also described herein are methods and compositions for treating a disease or condition characterized by impaired production of a full-length functional form of a protein or for treating a disease or condition characterized by a defective splicing in a subject.

What is claimed is: 
     
       1. A method of inducing processing of a partially processed mRNA transcript to facilitate removal of an entire retained intron to produce a fully processed mRNA transcript that encodes a functional form of a protein, the method comprising:
 (a) contacting an isolated polynucleic acid polymer to a target cell of a subject, wherein the polynucleic acid polymer is from about 10 to about 50 nucleotides in length; 
 (b) hybridizing the isolated polynucleic acid polymer to a wild-type target sequence of the partially processed mRNA transcript, wherein the polynucleic acid polymer comprises a sequence that is complementary to at least 10 contiguous bases of the wild-type target sequence, wherein the partially processed mRNA transcript is capable of encoding the functional form of a protein and comprises at least one entire retained intron, optionally interfering with one or more conformational transitions of canonical and noncanonical RNA structures or interacting with trans-acting factors that bind to an intron; 
 (c) removing the at least one entire retained intron from the partially processed mRNA transcript to produce the fully processed mRNA transcript that encodes the functional form of a protein; and 
 (d) translating the functional form of a protein from the fully processed mRNA transcript. 
 
     
     
       2. The method of  claim 1 , wherein the intron of step (b) is an INS intron. 
     
     
       3. The method of  claim 1 , wherein the partially processed mRNA transcript comprising the entire retained intron further induces a disease or condition or a predisposition to a disease or condition. 
     
     
       4. The method of  claim 3 , wherein the disease or condition is diabetes. 
     
     
       5. The method of  claim 1 , wherein the polynucleic acid polymer comprises an artificial nucleotide. 
     
     
       6. The method of  claim 1 , wherein the artificial nucleotide is selected from the group consisting of 2′-O-methyl, 2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl, 2′-deoxy, T-deoxy-2′-fluoro, 2′-O-aminopropyl (2′-O-AP), 2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl (2′-O-DMAP), T-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), 2′-O—N-methylacetamido (2′-O-NMA), a locked nucleic acid (LNA), an ethylene nucleic acid (ENA), a peptide nucleic acid (PNA), anhydrohexitol nucleic acid (HNA), a morpholino, a methylphosphonate nucleotide, a thiolphosphonate nucleotide, and a 2′-fluoro N3-P5′-phosphoramidite. 
     
     
       7. The method of  claim 1 , wherein the subject is human. 
     
     
       8. The method of  claim 1 , wherein the target sequence is a binding motif that forms a hairpin structure. 
     
     
       9. The method of  claim 1 , wherein the target sequence is between two G quadruplexes of a partially processed mRNA transcript. 
     
     
       10. The method of  claim 1 , wherein the target sequence is within the entire retained intron of the partially processed mRNA transcript. 
     
     
       11. The method of  claim 1 , wherein the target sequence does not form a G quadruplex. 
     
     
       12. The method of  claim 1 , wherein the target sequence is an intronic sequence. 
     
     
       13. The method of  claim 12 , wherein the intronic sequence comprises an intronic splicing regulatory element comprising a first CCC motif or a second CCC motif. 
     
     
       14. The method of  claim 1 , wherein the polynucleic acid polymer is from about 10 to about 30 nucleotides in length. 
     
     
       15. The method of  claim 1 , wherein the polynucleic acid polymer comprises a sequence that is at least 60% complementary to the wild-type target sequence of the partially processed mRNA transcript. 
     
     
       16. The method of  claim 1 , wherein the polynucleic acid polymer comprises a sequence that is complementary to a sequence with:
 (i) at least 80% sequence identity to at least 13 contiguous bases of SEQ ID NO: 46; 
 (ii) at least 10 contiguous bases of SEQ ID NO: 46; 
 (iii) at least 80% sequence identity to a sequence selected from the group consisting of SEQ ID NO: 6, SEQ ID NO: 9, SEQ ID NO: 12, SEQ ID NO: 15, SEQ ID NO: 18, SEQ ID NO: 21, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 30, SEQ ID NO: 33, SEQ ID NO: 36, SEQ ID NO: 39, SEQ ID NO: 42, and SEQ ID NO: 45; or 
 (iv) at least 60% sequence identity to SEQ ID NO: 3. 
 
     
     
       17. The method of  claim 1 , wherein the polynucleic acid polymer is modified at a nucleoside moiety, at a phosphate moiety, at a 5′ terminus, at a 3′ terminus, or a combination thereof. 
     
     
       18. The method of  claim 3 , wherein the disease or condition is a hereditary disease. 
     
     
       19. The method of  claim 1 , wherein the polynucleic acid polymer comprises a sequence having at least 80% sequence identity to at least 13 contiguous bases of a sequence selected from the group consisting of SEQ ID NOs: 47-434. 
     
     
       20. The method of any one of  claims 1 - 7 ,  8 - 13  and  14 - 19 , wherein the wild-type target sequence does not comprise a mutation-induced aberrant splice site.